Starting phenix.real_space_refine on Sun Apr 7 05:16:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6v1i_21012/04_2024/6v1i_21012_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 54 5.16 5 C 6129 2.51 5 N 1701 2.21 5 O 1827 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 9711 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "B" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "C" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "D" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "E" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "F" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "G" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Chain: "I" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1079 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 5, 'TRANS': 131} Time building chain proxies: 5.41, per 1000 atoms: 0.56 Number of scatterers: 9711 At special positions: 0 Unit cell: (133.434, 131.316, 67.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 54 16.00 O 1827 8.00 N 1701 7.00 C 6129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.46 Conformation dependent library (CDL) restraints added in 1.7 seconds 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2376 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 0 sheets defined 79.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 5 through 15 Processing helix chain 'A' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU A 28 " --> pdb=" O GLN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL A 42 " --> pdb=" O GLU A 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 48 " --> pdb=" O ALA A 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU A 49 " --> pdb=" O GLU A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 79 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN A 87 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE A 112 " --> pdb=" O ARG A 108 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA A 113 " --> pdb=" O PRO A 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE A 127 " --> pdb=" O ASP A 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 28 removed outlier: 3.839A pdb=" N LEU B 28 " --> pdb=" O GLN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL B 42 " --> pdb=" O GLU B 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU B 48 " --> pdb=" O ALA B 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 49 " --> pdb=" O GLU B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 94 removed outlier: 3.858A pdb=" N GLU B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA B 79 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN B 87 " --> pdb=" O ASN B 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY B 94 " --> pdb=" O ALA B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE B 112 " --> pdb=" O ARG B 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU C 28 " --> pdb=" O GLN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL C 42 " --> pdb=" O GLU C 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 48 " --> pdb=" O ALA C 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C 49 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU C 62 " --> pdb=" O ASP C 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA C 79 " --> pdb=" O LYS C 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN C 87 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY C 94 " --> pdb=" O ALA C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE C 112 " --> pdb=" O ARG C 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE C 127 " --> pdb=" O ASP C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 28 removed outlier: 3.839A pdb=" N LEU D 28 " --> pdb=" O GLN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL D 42 " --> pdb=" O GLU D 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 48 " --> pdb=" O ALA D 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU D 49 " --> pdb=" O GLU D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU D 62 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 79 " --> pdb=" O LYS D 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN D 87 " --> pdb=" O ASN D 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA D 113 " --> pdb=" O PRO D 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU E 28 " --> pdb=" O GLN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL E 42 " --> pdb=" O GLU E 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU E 48 " --> pdb=" O ALA E 44 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E 49 " --> pdb=" O GLU E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU E 62 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA E 79 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN E 87 " --> pdb=" O ASN E 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY E 94 " --> pdb=" O ALA E 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE E 112 " --> pdb=" O ARG E 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA E 113 " --> pdb=" O PRO E 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE E 127 " --> pdb=" O ASP E 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU F 28 " --> pdb=" O GLN F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL F 42 " --> pdb=" O GLU F 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU F 48 " --> pdb=" O ALA F 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU F 62 " --> pdb=" O ASP F 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA F 79 " --> pdb=" O LYS F 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN F 87 " --> pdb=" O ASN F 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY F 94 " --> pdb=" O ALA F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE F 112 " --> pdb=" O ARG F 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA F 113 " --> pdb=" O PRO F 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU G 28 " --> pdb=" O GLN G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 51 removed outlier: 3.715A pdb=" N VAL G 42 " --> pdb=" O GLU G 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU G 48 " --> pdb=" O ALA G 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU G 62 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA G 79 " --> pdb=" O LYS G 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN G 87 " --> pdb=" O ASN G 83 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY G 94 " --> pdb=" O ALA G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE G 112 " --> pdb=" O ARG G 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA G 113 " --> pdb=" O PRO G 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE G 127 " --> pdb=" O ASP G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU H 28 " --> pdb=" O GLN H 24 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL H 42 " --> pdb=" O GLU H 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU H 48 " --> pdb=" O ALA H 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 94 removed outlier: 3.858A pdb=" N GLU H 62 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA H 79 " --> pdb=" O LYS H 75 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASN H 87 " --> pdb=" O ASN H 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 108 through 137 removed outlier: 3.611A pdb=" N ILE H 112 " --> pdb=" O ARG H 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA H 113 " --> pdb=" O PRO H 109 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 28 removed outlier: 3.840A pdb=" N LEU I 28 " --> pdb=" O GLN I 24 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 51 removed outlier: 3.716A pdb=" N VAL I 42 " --> pdb=" O GLU I 38 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU I 48 " --> pdb=" O ALA I 44 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU I 49 " --> pdb=" O GLU I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 94 removed outlier: 3.859A pdb=" N GLU I 62 " --> pdb=" O ASP I 58 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA I 79 " --> pdb=" O LYS I 75 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ASN I 87 " --> pdb=" O ASN I 83 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 108 through 137 removed outlier: 3.612A pdb=" N ILE I 112 " --> pdb=" O ARG I 108 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA I 113 " --> pdb=" O PRO I 109 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE I 127 " --> pdb=" O ASP I 123 " (cutoff:3.500A) 702 hydrogen bonds defined for protein. 2106 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.16 Time building geometry restraints manager: 3.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3313 1.34 - 1.46: 1038 1.46 - 1.57: 5360 1.57 - 1.68: 0 1.68 - 1.80: 108 Bond restraints: 9819 Sorted by residual: bond pdb=" C SER I 4 " pdb=" N PHE I 5 " ideal model delta sigma weight residual 1.332 1.302 0.030 1.35e-02 5.49e+03 4.82e+00 bond pdb=" C SER E 4 " pdb=" N PHE E 5 " ideal model delta sigma weight residual 1.331 1.301 0.029 1.38e-02 5.25e+03 4.46e+00 bond pdb=" C SER D 4 " pdb=" N PHE D 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.41e+00 bond pdb=" C SER G 4 " pdb=" N PHE G 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.34e+00 bond pdb=" C SER C 4 " pdb=" N PHE C 5 " ideal model delta sigma weight residual 1.331 1.302 0.029 1.38e-02 5.25e+03 4.32e+00 ... (remaining 9814 not shown) Histogram of bond angle deviations from ideal: 98.72 - 105.24: 189 105.24 - 111.76: 4864 111.76 - 118.28: 2784 118.28 - 124.79: 5348 124.79 - 131.31: 63 Bond angle restraints: 13248 Sorted by residual: angle pdb=" C GLU B 97 " pdb=" N HIS B 98 " pdb=" CA HIS B 98 " ideal model delta sigma weight residual 121.03 124.60 -3.57 1.60e+00 3.91e-01 4.99e+00 angle pdb=" C GLU F 97 " pdb=" N HIS F 98 " pdb=" CA HIS F 98 " ideal model delta sigma weight residual 121.03 124.59 -3.56 1.60e+00 3.91e-01 4.96e+00 angle pdb=" C GLU I 97 " pdb=" N HIS I 98 " pdb=" CA HIS I 98 " ideal model delta sigma weight residual 121.03 124.59 -3.56 1.60e+00 3.91e-01 4.96e+00 angle pdb=" C GLU A 97 " pdb=" N HIS A 98 " pdb=" CA HIS A 98 " ideal model delta sigma weight residual 121.03 124.58 -3.55 1.60e+00 3.91e-01 4.93e+00 angle pdb=" C GLU G 97 " pdb=" N HIS G 98 " pdb=" CA HIS G 98 " ideal model delta sigma weight residual 121.03 124.57 -3.54 1.60e+00 3.91e-01 4.89e+00 ... (remaining 13243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 5850 13.54 - 27.08: 216 27.08 - 40.62: 126 40.62 - 54.16: 0 54.16 - 67.70: 9 Dihedral angle restraints: 6201 sinusoidal: 2574 harmonic: 3627 Sorted by residual: dihedral pdb=" CA LEU F 15 " pdb=" C LEU F 15 " pdb=" N GLY F 16 " pdb=" CA GLY F 16 " ideal model delta harmonic sigma weight residual 180.00 164.10 15.90 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU H 15 " pdb=" C LEU H 15 " pdb=" N GLY H 16 " pdb=" CA GLY H 16 " ideal model delta harmonic sigma weight residual 180.00 164.11 15.89 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA LEU C 15 " pdb=" C LEU C 15 " pdb=" N GLY C 16 " pdb=" CA GLY C 16 " ideal model delta harmonic sigma weight residual 180.00 164.12 15.88 0 5.00e+00 4.00e-02 1.01e+01 ... (remaining 6198 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 753 0.026 - 0.051: 446 0.051 - 0.076: 250 0.076 - 0.102: 83 0.102 - 0.127: 52 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA ILE I 105 " pdb=" N ILE I 105 " pdb=" C ILE I 105 " pdb=" CB ILE I 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA ILE C 105 " pdb=" N ILE C 105 " pdb=" C ILE C 105 " pdb=" CB ILE C 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE A 105 " pdb=" N ILE A 105 " pdb=" C ILE A 105 " pdb=" CB ILE A 105 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.00e-01 ... (remaining 1581 not shown) Planarity restraints: 1710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO C 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 99 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 99 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 98 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO E 99 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO E 99 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 99 " -0.023 5.00e-02 4.00e+02 ... (remaining 1707 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 3982 2.98 - 3.46: 10365 3.46 - 3.94: 14573 3.94 - 4.42: 17338 4.42 - 4.90: 26850 Nonbonded interactions: 73108 Sorted by model distance: nonbonded pdb=" OD1 ASN E 87 " pdb=" NE2 HIS E 98 " model vdw 2.505 2.520 nonbonded pdb=" OD1 ASN G 87 " pdb=" NE2 HIS G 98 " model vdw 2.505 2.520 nonbonded pdb=" OD1 ASN F 87 " pdb=" NE2 HIS F 98 " model vdw 2.505 2.520 nonbonded pdb=" OD1 ASN A 87 " pdb=" NE2 HIS A 98 " model vdw 2.505 2.520 nonbonded pdb=" OD1 ASN I 87 " pdb=" NE2 HIS I 98 " model vdw 2.505 2.520 ... (remaining 73103 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.790 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 27.750 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 9819 Z= 0.452 Angle : 0.905 5.817 13248 Z= 0.507 Chirality : 0.044 0.127 1584 Planarity : 0.006 0.042 1710 Dihedral : 9.434 67.700 3825 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.19), residues: 1215 helix: -2.88 (0.11), residues: 972 sheet: None (None), residues: 0 loop : 0.17 (0.39), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS G 98 PHE 0.008 0.002 PHE C 73 TYR 0.006 0.002 TYR E 13 ARG 0.009 0.001 ARG F 69 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 322 time to evaluate : 1.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8579 (m-30) cc_final: 0.8298 (m-30) REVERT: A 117 ASP cc_start: 0.8466 (t0) cc_final: 0.8215 (t0) REVERT: B 72 ILE cc_start: 0.9547 (mm) cc_final: 0.9300 (mm) REVERT: C 72 ILE cc_start: 0.9479 (mm) cc_final: 0.9255 (mm) REVERT: D 72 ILE cc_start: 0.9506 (mm) cc_final: 0.9236 (mm) REVERT: E 76 ASP cc_start: 0.8587 (m-30) cc_final: 0.8345 (m-30) REVERT: F 72 ILE cc_start: 0.9539 (mm) cc_final: 0.9300 (mt) REVERT: F 123 ASP cc_start: 0.8895 (t0) cc_final: 0.8582 (t0) REVERT: G 72 ILE cc_start: 0.9494 (mm) cc_final: 0.9263 (mt) REVERT: G 117 ASP cc_start: 0.8604 (t0) cc_final: 0.8201 (t0) REVERT: H 72 ILE cc_start: 0.9501 (mm) cc_final: 0.9294 (mm) REVERT: H 76 ASP cc_start: 0.8573 (m-30) cc_final: 0.8276 (m-30) REVERT: I 1 MET cc_start: 0.6519 (ttm) cc_final: 0.4992 (mtp) REVERT: I 24 GLN cc_start: 0.9317 (mt0) cc_final: 0.9083 (mt0) REVERT: I 72 ILE cc_start: 0.9536 (mm) cc_final: 0.9292 (mm) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.3697 time to fit residues: 145.3998 Evaluate side-chains 180 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.9980 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.3980 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 35 optimal weight: 0.3980 chunk 55 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 106 optimal weight: 0.1980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** E 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9819 Z= 0.179 Angle : 0.538 4.085 13248 Z= 0.289 Chirality : 0.038 0.119 1584 Planarity : 0.005 0.028 1710 Dihedral : 3.816 10.459 1350 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.42 % Allowed : 10.16 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1215 helix: 0.72 (0.15), residues: 972 sheet: None (None), residues: 0 loop : 0.95 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 98 PHE 0.004 0.001 PHE E 73 TYR 0.004 0.001 TYR C 88 ARG 0.007 0.001 ARG G 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 1.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 ASP cc_start: 0.8528 (m-30) cc_final: 0.8269 (m-30) REVERT: A 117 ASP cc_start: 0.8522 (t0) cc_final: 0.8310 (t0) REVERT: A 120 MET cc_start: 0.8718 (mtp) cc_final: 0.8376 (mtp) REVERT: E 4 SER cc_start: 0.8668 (m) cc_final: 0.8351 (p) REVERT: E 75 LYS cc_start: 0.9298 (mmmm) cc_final: 0.8937 (mmtt) REVERT: E 76 ASP cc_start: 0.8486 (m-30) cc_final: 0.8254 (m-30) REVERT: E 92 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8018 (tmm) REVERT: F 117 ASP cc_start: 0.8464 (t0) cc_final: 0.8212 (t0) REVERT: F 120 MET cc_start: 0.8650 (mtp) cc_final: 0.8394 (mtp) REVERT: G 33 LYS cc_start: 0.8344 (ptmm) cc_final: 0.8016 (ttpp) REVERT: G 115 MET cc_start: 0.9190 (mmt) cc_final: 0.8983 (mmt) REVERT: G 117 ASP cc_start: 0.8596 (t0) cc_final: 0.8298 (t0) REVERT: G 120 MET cc_start: 0.8779 (mtp) cc_final: 0.8444 (mtt) REVERT: H 4 SER cc_start: 0.8593 (m) cc_final: 0.8329 (p) REVERT: H 76 ASP cc_start: 0.8447 (m-30) cc_final: 0.8110 (m-30) REVERT: I 8 ARG cc_start: 0.9187 (mmm-85) cc_final: 0.8875 (mmm-85) REVERT: I 117 ASP cc_start: 0.8463 (t0) cc_final: 0.8240 (t0) outliers start: 36 outliers final: 31 residues processed: 235 average time/residue: 0.3419 time to fit residues: 100.7634 Evaluate side-chains 187 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 155 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 29 optimal weight: 10.0000 chunk 106 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN ** A 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 GLN D 82 GLN E 83 ASN ** F 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 83 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 GLN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9819 Z= 0.160 Angle : 0.475 5.972 13248 Z= 0.248 Chirality : 0.036 0.125 1584 Planarity : 0.004 0.025 1710 Dihedral : 3.330 9.719 1350 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 3.32 % Allowed : 10.83 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.25 (0.23), residues: 1215 helix: 2.37 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.46 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 41 PHE 0.007 0.001 PHE E 73 TYR 0.005 0.001 TYR E 81 ARG 0.005 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 169 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9433 (mmmt) cc_final: 0.9117 (tppt) REVERT: B 135 LYS cc_start: 0.9559 (tptp) cc_final: 0.9028 (ptpp) REVERT: E 4 SER cc_start: 0.8607 (m) cc_final: 0.8379 (p) REVERT: E 76 ASP cc_start: 0.8504 (m-30) cc_final: 0.8266 (m-30) REVERT: E 92 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8070 (tmm) REVERT: E 135 LYS cc_start: 0.8834 (ptpp) cc_final: 0.8557 (ptpp) REVERT: G 33 LYS cc_start: 0.8315 (ptmm) cc_final: 0.7928 (ttpp) REVERT: G 117 ASP cc_start: 0.8571 (t0) cc_final: 0.8353 (t0) REVERT: H 76 ASP cc_start: 0.8612 (m-30) cc_final: 0.8262 (m-30) REVERT: I 83 ASN cc_start: 0.9146 (OUTLIER) cc_final: 0.8873 (t0) outliers start: 35 outliers final: 31 residues processed: 194 average time/residue: 0.3327 time to fit residues: 81.2480 Evaluate side-chains 176 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 83 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 105 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 11 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 chunk 71 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 101 optimal weight: 0.0040 chunk 30 optimal weight: 0.9980 chunk 94 optimal weight: 9.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 ASN F 82 GLN G 82 GLN ** G 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 9819 Z= 0.136 Angle : 0.469 8.723 13248 Z= 0.235 Chirality : 0.035 0.127 1584 Planarity : 0.004 0.025 1710 Dihedral : 3.091 9.395 1350 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.32 % Allowed : 11.40 % Favored : 85.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.15 (0.23), residues: 1215 helix: 3.05 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.56 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 98 PHE 0.005 0.001 PHE F 73 TYR 0.004 0.001 TYR H 81 ARG 0.005 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 167 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9445 (mmmt) cc_final: 0.9216 (tppt) REVERT: C 120 MET cc_start: 0.8839 (mtp) cc_final: 0.8491 (mtp) REVERT: D 4 SER cc_start: 0.8541 (m) cc_final: 0.8314 (p) REVERT: D 8 ARG cc_start: 0.9352 (mmm-85) cc_final: 0.9056 (mmm-85) REVERT: E 76 ASP cc_start: 0.8544 (m-30) cc_final: 0.8321 (m-30) REVERT: E 92 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8259 (tmm) REVERT: G 4 SER cc_start: 0.8490 (m) cc_final: 0.8229 (p) REVERT: G 8 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.8979 (mmm-85) REVERT: G 33 LYS cc_start: 0.8308 (ptmm) cc_final: 0.7956 (ttpp) REVERT: G 117 ASP cc_start: 0.8546 (t0) cc_final: 0.8295 (t0) REVERT: H 8 ARG cc_start: 0.9326 (mmm-85) cc_final: 0.9001 (mmm-85) REVERT: H 75 LYS cc_start: 0.9428 (mmmt) cc_final: 0.9185 (tppt) REVERT: H 76 ASP cc_start: 0.8597 (m-30) cc_final: 0.8359 (m-30) REVERT: H 83 ASN cc_start: 0.9140 (OUTLIER) cc_final: 0.8933 (t0) outliers start: 35 outliers final: 32 residues processed: 192 average time/residue: 0.3438 time to fit residues: 82.6308 Evaluate side-chains 174 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 140 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 123 ASP Chi-restraints excluded: chain B residue 3 VAL Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 92 MET Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 83 ASN Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 0.4980 chunk 101 optimal weight: 6.9990 chunk 28 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 83 ASN ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8881 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9819 Z= 0.192 Angle : 0.522 9.689 13248 Z= 0.258 Chirality : 0.036 0.125 1584 Planarity : 0.004 0.025 1710 Dihedral : 3.040 10.177 1350 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.27 % Allowed : 12.44 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.56 (0.24), residues: 1215 helix: 3.35 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.68 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 98 PHE 0.009 0.001 PHE F 73 TYR 0.007 0.001 TYR I 81 ARG 0.005 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 141 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9449 (mmmt) cc_final: 0.9172 (tppt) REVERT: A 115 MET cc_start: 0.9158 (mmm) cc_final: 0.8905 (tpp) REVERT: A 135 LYS cc_start: 0.9540 (tptp) cc_final: 0.9068 (ptpp) REVERT: C 135 LYS cc_start: 0.9475 (tptp) cc_final: 0.9026 (ptpp) REVERT: D 4 SER cc_start: 0.8607 (m) cc_final: 0.8396 (p) REVERT: E 76 ASP cc_start: 0.8637 (m-30) cc_final: 0.8436 (m-30) REVERT: G 117 ASP cc_start: 0.8625 (t0) cc_final: 0.8315 (t0) REVERT: H 76 ASP cc_start: 0.8669 (m-30) cc_final: 0.8377 (m-30) REVERT: I 8 ARG cc_start: 0.9266 (mmm-85) cc_final: 0.8935 (mmm-85) outliers start: 45 outliers final: 29 residues processed: 172 average time/residue: 0.2983 time to fit residues: 65.9667 Evaluate side-chains 169 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 2 SER Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 3 VAL Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 0.1980 chunk 22 optimal weight: 8.9990 chunk 66 optimal weight: 0.0870 chunk 27 optimal weight: 0.3980 chunk 113 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 52 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 109 optimal weight: 20.0000 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.5041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9819 Z= 0.137 Angle : 0.501 10.306 13248 Z= 0.245 Chirality : 0.035 0.118 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.941 9.010 1350 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.32 % Allowed : 12.16 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.86 (0.24), residues: 1215 helix: 3.55 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.81 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 98 PHE 0.005 0.001 PHE B 73 TYR 0.004 0.000 TYR H 88 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 151 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 ARG cc_start: 0.9318 (mmm-85) cc_final: 0.9031 (mmm-85) REVERT: A 75 LYS cc_start: 0.9456 (mmmt) cc_final: 0.9169 (tppt) REVERT: A 135 LYS cc_start: 0.9457 (tptp) cc_final: 0.8982 (ptpp) REVERT: B 8 ARG cc_start: 0.9403 (mmm-85) cc_final: 0.9132 (mmm-85) REVERT: C 135 LYS cc_start: 0.9491 (tptp) cc_final: 0.9095 (ptpp) REVERT: D 8 ARG cc_start: 0.9329 (mmm-85) cc_final: 0.9079 (mmm-85) REVERT: D 120 MET cc_start: 0.9043 (mpp) cc_final: 0.8779 (mpp) REVERT: E 135 LYS cc_start: 0.9564 (tptp) cc_final: 0.9020 (ptpp) REVERT: F 75 LYS cc_start: 0.9416 (mmmt) cc_final: 0.9134 (tppt) REVERT: G 4 SER cc_start: 0.8623 (m) cc_final: 0.8396 (p) REVERT: G 8 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.9012 (mmm-85) REVERT: G 117 ASP cc_start: 0.8481 (t0) cc_final: 0.8238 (t0) REVERT: H 8 ARG cc_start: 0.9311 (mmm-85) cc_final: 0.9007 (mmm-85) REVERT: H 76 ASP cc_start: 0.8634 (m-30) cc_final: 0.8400 (m-30) REVERT: H 135 LYS cc_start: 0.9472 (tptp) cc_final: 0.9037 (ptpp) REVERT: I 8 ARG cc_start: 0.9226 (mmm-85) cc_final: 0.9007 (mmm-85) outliers start: 35 outliers final: 27 residues processed: 175 average time/residue: 0.3274 time to fit residues: 72.9426 Evaluate side-chains 167 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 140 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 6 ARG Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 12 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 63 optimal weight: 0.6980 chunk 112 optimal weight: 0.9990 chunk 70 optimal weight: 20.0000 chunk 68 optimal weight: 5.9990 chunk 52 optimal weight: 10.0000 chunk 69 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN ** B 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 83 ASN D 132 ASN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9819 Z= 0.145 Angle : 0.512 11.017 13248 Z= 0.248 Chirality : 0.036 0.118 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.901 9.425 1350 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.42 % Allowed : 13.20 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.03 (0.23), residues: 1215 helix: 3.67 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.86 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.007 0.001 PHE D 73 TYR 0.004 0.000 TYR E 81 ARG 0.005 0.000 ARG F 8 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 142 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9206 (tppt) REVERT: B 8 ARG cc_start: 0.9409 (mmm-85) cc_final: 0.9060 (mmm-85) REVERT: D 8 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.9073 (mmm-85) REVERT: G 4 SER cc_start: 0.8679 (m) cc_final: 0.8456 (p) REVERT: G 8 ARG cc_start: 0.9292 (mmm-85) cc_final: 0.9021 (mmm-85) REVERT: G 117 ASP cc_start: 0.8441 (t0) cc_final: 0.8224 (t0) REVERT: H 8 ARG cc_start: 0.9330 (mmm-85) cc_final: 0.9013 (mmm-85) REVERT: H 76 ASP cc_start: 0.8651 (m-30) cc_final: 0.8399 (m-30) REVERT: H 120 MET cc_start: 0.9071 (mpp) cc_final: 0.8452 (mpp) REVERT: H 135 LYS cc_start: 0.9451 (tptp) cc_final: 0.9014 (ptpp) REVERT: I 8 ARG cc_start: 0.9259 (mmm-85) cc_final: 0.8988 (mmm-85) outliers start: 36 outliers final: 31 residues processed: 167 average time/residue: 0.2906 time to fit residues: 62.9227 Evaluate side-chains 166 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 2 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 67 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 88 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.5243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9819 Z= 0.160 Angle : 0.547 11.382 13248 Z= 0.266 Chirality : 0.036 0.132 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.884 9.397 1350 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.42 % Allowed : 14.06 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.99 (0.23), residues: 1215 helix: 3.64 (0.16), residues: 963 sheet: None (None), residues: 0 loop : 1.88 (0.42), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS F 98 PHE 0.009 0.001 PHE D 73 TYR 0.006 0.000 TYR C 81 ARG 0.007 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9480 (mmmt) cc_final: 0.9206 (tppt) REVERT: B 8 ARG cc_start: 0.9400 (mmm-85) cc_final: 0.9060 (mmm-85) REVERT: D 8 ARG cc_start: 0.9321 (mmm-85) cc_final: 0.9065 (mmm-85) REVERT: E 117 ASP cc_start: 0.8139 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: G 4 SER cc_start: 0.8703 (m) cc_final: 0.8476 (p) REVERT: G 8 ARG cc_start: 0.9298 (mmm-85) cc_final: 0.9035 (mmm-85) REVERT: G 117 ASP cc_start: 0.8456 (t0) cc_final: 0.8224 (t0) REVERT: H 76 ASP cc_start: 0.8663 (m-30) cc_final: 0.8398 (m-30) REVERT: H 120 MET cc_start: 0.9057 (mpp) cc_final: 0.8473 (mpp) REVERT: H 124 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.8307 (mp10) REVERT: H 135 LYS cc_start: 0.9486 (tptp) cc_final: 0.9024 (ptpp) REVERT: I 8 ARG cc_start: 0.9271 (mmm-85) cc_final: 0.8984 (mmm-85) outliers start: 36 outliers final: 29 residues processed: 162 average time/residue: 0.2929 time to fit residues: 62.3135 Evaluate side-chains 170 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 139 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain B residue 117 ASP Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain E residue 117 ASP Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 chunk 32 optimal weight: 0.6980 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8868 moved from start: 0.5314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9819 Z= 0.153 Angle : 0.553 12.436 13248 Z= 0.270 Chirality : 0.036 0.122 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.864 9.330 1350 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.85 % Allowed : 14.25 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.23), residues: 1215 helix: 3.49 (0.16), residues: 981 sheet: None (None), residues: 0 loop : 2.06 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 98 PHE 0.006 0.001 PHE B 73 TYR 0.003 0.000 TYR H 88 ARG 0.007 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 140 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9470 (mmmt) cc_final: 0.9208 (tppt) REVERT: A 117 ASP cc_start: 0.8414 (t0) cc_final: 0.8134 (m-30) REVERT: D 8 ARG cc_start: 0.9335 (mmm-85) cc_final: 0.9068 (mmm-85) REVERT: E 8 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.8964 (mmm-85) REVERT: F 120 MET cc_start: 0.9274 (mpp) cc_final: 0.9057 (mpp) REVERT: G 8 ARG cc_start: 0.9296 (mmm-85) cc_final: 0.9040 (mmm-85) REVERT: H 8 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.8976 (mmm-85) REVERT: H 135 LYS cc_start: 0.9489 (tptp) cc_final: 0.9115 (ptpp) REVERT: I 8 ARG cc_start: 0.9274 (mmm-85) cc_final: 0.8988 (mmm-85) outliers start: 30 outliers final: 29 residues processed: 163 average time/residue: 0.2982 time to fit residues: 63.3800 Evaluate side-chains 165 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 111 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 52 optimal weight: 10.0000 chunk 77 optimal weight: 0.8980 chunk 116 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 73 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN ** D 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8871 moved from start: 0.5371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9819 Z= 0.158 Angle : 0.575 12.852 13248 Z= 0.278 Chirality : 0.037 0.124 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.869 10.225 1350 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.32 % Allowed : 14.15 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.89 (0.23), residues: 1215 helix: 3.48 (0.16), residues: 981 sheet: None (None), residues: 0 loop : 2.11 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 98 PHE 0.007 0.001 PHE D 73 TYR 0.003 0.000 TYR H 88 ARG 0.007 0.000 ARG A 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2430 Ramachandran restraints generated. 1215 Oldfield, 0 Emsley, 1215 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 LYS cc_start: 0.9478 (mmmt) cc_final: 0.9202 (tppt) REVERT: A 117 ASP cc_start: 0.8371 (t0) cc_final: 0.8162 (m-30) REVERT: B 8 ARG cc_start: 0.9396 (mmm-85) cc_final: 0.9019 (mmm-85) REVERT: D 8 ARG cc_start: 0.9343 (mmm-85) cc_final: 0.9055 (mmm-85) REVERT: F 120 MET cc_start: 0.9285 (mpp) cc_final: 0.9051 (mpp) REVERT: G 8 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.9041 (mmm-85) REVERT: H 8 ARG cc_start: 0.9342 (mmm-85) cc_final: 0.8967 (mmm-85) REVERT: I 8 ARG cc_start: 0.9291 (mmm-85) cc_final: 0.8987 (mmm-85) REVERT: I 135 LYS cc_start: 0.9013 (OUTLIER) cc_final: 0.8763 (ptpp) outliers start: 35 outliers final: 29 residues processed: 165 average time/residue: 0.3008 time to fit residues: 63.9126 Evaluate side-chains 165 residues out of total 1053 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 135 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 SER Chi-restraints excluded: chain A residue 35 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 35 THR Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 105 ILE Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 83 ASN Chi-restraints excluded: chain C residue 105 ILE Chi-restraints excluded: chain D residue 35 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 105 ILE Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 117 ASP Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 105 ILE Chi-restraints excluded: chain H residue 124 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 135 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 92 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 17 optimal weight: 0.9980 chunk 81 optimal weight: 7.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.039904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2536 r_free = 0.2536 target = 0.029120 restraints weight = 57900.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.030094 restraints weight = 34691.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.030723 restraints weight = 25735.768| |-----------------------------------------------------------------------------| r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.5384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9819 Z= 0.182 Angle : 0.605 13.097 13248 Z= 0.295 Chirality : 0.038 0.125 1584 Planarity : 0.004 0.025 1710 Dihedral : 2.876 9.356 1350 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.94 % Allowed : 14.91 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.23), residues: 1215 helix: 3.43 (0.16), residues: 981 sheet: None (None), residues: 0 loop : 2.20 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS H 98 PHE 0.008 0.001 PHE C 73 TYR 0.009 0.001 TYR C 81 ARG 0.007 0.000 ARG A 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2098.23 seconds wall clock time: 39 minutes 8.98 seconds (2348.98 seconds total)